Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species

Wenjun Zhou, Nan Zhang, Kaichi Huang, Hongzhou Lin, Jie Tu, Chenqing Zheng, Pinjia Que, Chung Yu Chiang, Jonathan Martinez, Halimubieke Naerhulan, Tamás Székely, Zhengwang Zhang, Yang Liu

Research output: Contribution to journalArticlepeer-review

Abstract

Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.

Original languageEnglish
Article numbermsae006
JournalMolecular Biology and Evolution
Volume41
Issue number2
Early online date16 Jan 2024
DOIs
Publication statusPublished - 29 Feb 2024

Data Availability Statement

The filtered VCF dataset used in this study containing 104 individuals (including 3 individuals representing the Azores Islands outgroup) is available in Dryad Digital Repository at https://doi.org/10.5061/dryad.4f4qrfjjp. Custom scripts will be made available by the authors on request

Keywords

  • contact zone
  • gene flow
  • genomic islands
  • incipient speciation
  • population genomics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Fingerprint

Dive into the research topics of 'Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species'. Together they form a unique fingerprint.

Cite this